Roses are the most popular cut flowers that are widely used in various occasions and celebrations, yet can also be easily infected by grey mold caused by Botrytis cinerea; a notorious pathogen in the cut flower industry. A wide range of methods, including fungicides, have been used to control B. cinerea. Environmentally benign methods are increasingly sought after to minimize disease incidence. In this study, we evaluated 10 strains of Bacillus across eight species for their action against B. cinerea. Strains TM22A (Bacillus altitudinis) and S2 (Bacillus subtilis) were identified to be effective in disease suppression. Lipopeptides (LPs) were isolated from two strains, and their activity for inhibiting the growth of B. cinerea was tested. Additionally, methyl jasmonate (MeJA), a natural growth regulator, was evaluated for disease suppression using a in planta assay. Subsequently, LPs from TM22A and MeJA, alone or in combination, were evaluated for disease occurrence in cut rose flowers. Results showed that either LPs or MeJA at concentrations of 250 μmol/L significantly reduced lesion size and disease incidence. The combined application of LPs from TM22A with MeJA further reduced the disease occurrence in cut rose flowers. Furthermore, the activities of POD, PPO, PAL, CAT, and SOD enzymes were much higher in flowers treated with combined application of LPs from TM22A with MeJA. The enhanced suppression of B. cinerea is attributed to the antifungal effects of LPs and MeJA and activation of antioxidant enzymes. This study suggests that the combined application of LPs from TM22A with MeJA could be an environmentally friendly approach for control of grey mold disease in cut roses.